Contacts of the strand formed by residues 114 - 125 (chain K) in PDB entry 5HJD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 114 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15K HIS* 3.3 33.2 - - + +
16K ARG* 3.2 8.3 - - - +
17K ALA* 2.8 45.5 + - + +
105K PHE* 3.5 28.7 - - + +
107K HIS* 3.4 50.7 - - + +
113K PRO* 1.3 72.7 - - - +
115K ASN* 1.3 64.2 + - - +
116K HIS* 4.1 4.9 - - + +
115T ASN* 5.2 1.4 + - - -
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Residues in contact with ASN 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K HIS 3.8 2.3 - - - +
16K ARG* 3.3 17.6 - - - +
35K PHE* 5.8 2.9 - - - -
113K PRO 3.7 4.1 + - - +
114K VAL* 1.3 74.2 - - - +
116K HIS* 1.3 62.1 + - - +
16T ARG* 5.6 7.5 - - - +
37T ARG* 4.5 9.0 + - - +
115T ASN* 3.1 57.8 + - - +
116T HIS 4.5 0.6 + - - -
117T LEU* 3.1 37.8 - - + +
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Residues in contact with HIS 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K GLY* 3.2 3.8 - - - -
15K HIS* 3.1 53.8 + - + +
35K PHE* 4.7 2.6 - - - -
102K TYR* 3.7 15.6 + + - -
103K ASP 6.0 0.4 - - - -
105K PHE* 3.7 30.4 - + + -
114K VAL* 4.0 0.6 - - + -
115K ASN* 1.3 76.1 + - - +
117K LEU* 1.3 79.6 + - - +
118K ARG* 4.1 17.4 - - + +
12T GLU* 5.9 1.3 - - - -
40T GLU* 5.1 15.9 + - + +
117T LEU* 4.5 0.9 - - - -
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Residues in contact with LEU 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K GLU* 4.2 16.6 - - + +
13K LEU 3.6 15.9 - - - +
35K PHE* 3.9 26.7 - - + -
37K ARG* 3.7 11.4 - - - +
115K ASN 4.2 1.2 + - - -
116K HIS* 1.3 86.0 + - - +
118K ARG* 1.3 61.1 + - - +
119K CYS* 4.2 0.8 + - - -
12T GLU* 4.2 16.1 + - + +
39T PRO* 6.0 0.9 - - - +
117T LEU* 3.3 52.5 - - + +
118T ARG* 3.8 2.2 - - - +
119T CYS* 3.6 33.4 - - - +
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Residues in contact with ARG 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K GLU* 3.6 1.5 - - - -
13K LEU* 2.6 60.9 + - + +
100K PHE* 3.7 29.0 - - - +
101K ASP 3.7 22.6 + - - +
102K TYR* 4.0 21.8 - - + +
103K ASP 4.7 1.8 - - - +
116K HIS* 4.1 16.4 - - + +
117K LEU* 1.3 75.5 - - - +
119K CYS* 1.3 63.8 + - - +
120K GLU* 2.8 32.1 + - + +
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Residues in contact with CYS 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K LYS* 6.3 3.1 - - + -
11K LEU 3.7 5.4 - - - +
12K GLU* 4.1 17.9 - - + -
118K ARG* 1.3 74.4 - - - +
120K GLU* 1.3 70.1 + - - +
10T LYS* 5.8 2.3 + - - -
119T CYS* 2.0 62.0 - - + -
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Residues in contact with GLU 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K LYS* 3.7 3.1 - - - +
11K LEU* 2.8 46.9 + - + +
13K LEU* 3.7 26.7 - - + -
100K PHE* 3.7 25.5 - - + -
118K ARG* 2.8 37.8 + - + +
119K CYS* 1.3 80.7 - - - +
121K LYS* 1.3 64.9 + - - +
122K LEU* 4.0 0.6 + - + -
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Residues in contact with LYS 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K GLN* 3.3 39.9 + - + +
9K VAL 3.6 11.0 - - - +
10K LYS* 4.7 11.7 - - + +
120K GLU* 1.3 77.3 + - - +
122K LEU* 1.3 74.0 + - - +
123K THR* 4.3 12.1 + - - +
8T GLN* 5.8 2.2 + - - -
121T LYS* 5.9 7.6 - - - +
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Residues in contact with LEU 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K VAL 3.5 1.0 - - - +
8K GLN* 3.3 7.6 - - - +
9K VAL* 2.8 56.0 + - + +
11K LEU* 3.6 33.0 - - + -
47K PHE* 5.1 0.2 - - + -
89K PHE* 4.2 15.5 - - + -
98K VAL* 3.9 25.4 - - + -
100K PHE* 3.9 25.4 - - + -
120K GLU* 4.9 2.7 - - + +
121K LYS* 1.3 80.4 - - - +
123K THR* 1.3 61.5 + - - +
124K PHE* 3.7 9.4 - - + -
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Residues in contact with THR 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ALA* 4.6 13.5 - - + -
7K VAL 3.7 4.7 - - - +
8K GLN* 4.6 10.0 + - + +
121K LYS* 4.3 15.1 + - - +
122K LEU* 1.3 76.5 + - - +
124K PHE* 1.3 66.0 - - - +
125K ASN* 3.9 30.5 + - - +
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Residues in contact with PHE 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K CYS 3.3 2.8 - - - +
6K ALA* 3.4 2.1 - - - -
7K VAL* 2.9 51.1 + - + +
9K VAL* 3.5 28.0 - - + -
47K PHE* 5.2 0.2 - + - -
89K PHE* 3.8 43.1 - + - -
91K ASN* 5.2 0.4 - - - -
95K PRO* 4.8 17.9 - - + -
122K LEU* 3.7 14.8 - - + -
123K THR* 1.3 74.8 - - - +
125K ASN* 1.3 62.2 + - - +
127K PRO* 3.8 11.5 - - + +
131K PHE* 3.7 25.1 - + - -
135K LEU* 3.9 30.7 - - + -
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Residues in contact with ASN 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K CYS 3.2 7.7 - - - +
6K ALA* 4.6 6.1 - - - +
123K THR* 3.9 28.4 + - - +
124K PHE* 1.3 72.7 - - - +
126K ASN* 1.3 82.2 + - - +
127K PRO* 3.5 1.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il